Group Water_and_ions referenced in the .mdp file was not found

User discussions
1

GROMACS version:
GROMACS modification: Yes/No

Hello, I have got an error about water_ions not found

Firstly I have an error about NA molecules

ERROR 1 [file topol.top, line 109640]:
No such moleculetype NA
I have posted a question about it (ERROR No such moleculetype NA)

Then I have change their name from NA in topol and solv_ion files to SOD, because when I check the ion.itp file I found this lines:

[ moleculetype ]
;Sodium Ion
; molname nrexcl
SOD 3
so, I assume that I have to change the name of NA to SOD.
The code run correctly and other next lines

but when I was in code line: I have used the line gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr
I got an error:
this is the whole message

          :-) GROMACS - gmx grompp, 2020.1-Ubuntu-2020.1-1 (-:

                        GROMACS is written by:
 Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd

Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /mnt/d/Articles/Y MDs/Works/2022/Linani
Command line:
gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr

Ignoring obsolete mdp entry ‘title’
Ignoring obsolete mdp entry ‘ns_type’
Setting the LD random seed to 1848058077
Generated 167799 of the 167910 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 117519 of the 167910 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein_chain_C’
turning H bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘cp11’
turning H bonds into constraints…
Excluding 2 bonded neighbours molecule type ‘SOL’
turning H bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘SOD’
turning H bonds into constraints…
Setting gen_seed to -458316911
Velocities were taken from a Maxwell distribution at 300 K

Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/readir.cpp (line 2701)

Fatal error:
Group Water_and_ions referenced in the .mdp file was not found in the index
file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the ‘-n’ option
of grompp.

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

How to fix this error?

2

Did you recreate the index file after the “SOD to NA” change?

3

Dear Teslim
I did not create the index file
how to create it?

4

use the make_ndx with the trajectory or coordinate file to generate the index

5

Fatal error:
Group Water_and_ions referenced in the .mdp file was not found in the index
file.

I am facing a similar error while doing the NVT step. Please help.

6

You need to create the index file for “Protein_Lig” and “Ion_Water” during equilibration stage.

7

My problem is the same.
“Fatal error: Group Water_and_ions referenced in the .mdp file was not found in the index
file.”
Any sugestion other than that??

8

Ashish, you say in the part of the command “gmx make_ndx -f em.gro -o index.ndx”??
I need to create a file by selecting Protein_Ligand and another Water_ions using this command twice, am I right?
Did it work for you?
I’m amateur, sorry.

9

If you changed NA to SOD then you need to make a new index file to include SOD. And then replace Water_and_ions with SOD_Water in the.mdp file.

10

Perfect!
Thanks, really.

11

NVT_tpr_problem
NVT_tpr_problem1007×818 21.3 KB

i am facing the same problem in NVT.tpr step ; plz help me .

12

You need to make sure the group is included in the index file. You should be able to use gmx make_ndx to create the group and specify which atoms should be in the group. If you’d already made that group previously, double check the index.ndx file to make sure the group is under the same name as what is called in the mdp file.